first add

utils/test_smart.py

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+from rdkit import Chem
+from joblib import Parallel, delayed
+import logging
+
+# 定义日志配置
+logging.basicConfig(
+    filename="rgroup_matching.log",
+    level=logging.INFO,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+)
+
+# 定义 SMARTS 模式
+macro = Chem.MolFromSmarts("[r12,r13,r14,r15,r16,r17,r18,r19,r20]([#8][#6](=[#8]))")
+
+# 读取 SMI 文件
+smi_file = "/home/mambauser/LillyMol/test/1M_stratsampled_V1B.smi"
+with open(smi_file, 'r') as f:
+    SMILES_list = [line.strip() for line in f if line.strip()]
+
+logging.info(f"Loaded {len(SMILES_list)} molecules from {smi_file}.")
+
+# 匹配函数
+def match_smarts(smiles):
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is None:
+        return smiles, None  # 无效分子
+    result = mol.GetSubstructMatches(macro)
+    return smiles, result
+
+# 使用 joblib 并行处理
+logging.info("Starting SMARTS matching...")
+results = Parallel(n_jobs=-1)(delayed(match_smarts)(s) for s in SMILES_list)
+
+# 分离成功和失败的分子
+success = [smiles for smiles, result in results if result]
+fail = [smiles for smiles, result in results if not result]
+
+# 统计结果
+total = len(success) + len(fail)
+success_rate = len(success) / total * 100 if total > 0 else 0
+
+# 保存日志信息
+logging.info(f"Total molecules: {total}")
+logging.info(f"Success: {len(success)}")
+logging.info(f"Fail: {len(fail)}")
+logging.info(f"Success rate: {success_rate:.2f}%")
+
+print(f"Total molecules: {total}")
+print(f"Success: {len(success)}")
+print(f"Fail: {len(fail)}")
+print(f"Success rate: {success_rate:.2f}%")
+
+# 将失败的分子写入到一个 SMI 文件
+fail_smi_file = "fail_molecules.smi"
+with open(fail_smi_file, "w") as ff:
+    for smiles in fail:
+        ff.write(smiles + "\n")
+
+logging.info(f"Failed molecules written to {fail_smi_file}.")
+print(f"Failed molecules written to {fail_smi_file}.")